Contacts of the strand formed by residues 205 - 210 (chain A) in PDB entry 3QG2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LEU* 3.7 27.9 - - + +
177A LYS* 4.6 12.1 - - + +
179A ILE* 2.9 48.3 + - + +
180A LYS 4.5 2.2 - - - -
182A ILE* 4.4 11.9 - - + -
200A ILE* 3.6 31.0 - - + +
201A ASN* 2.9 6.4 + - + +
202A GLU* 3.3 20.6 - - - +
203A ASN 3.6 0.4 - - - -
204A GLU* 1.3 97.7 - - + +
206A GLN* 1.3 64.6 + - - +
226A TYR* 4.2 17.2 - - + -
227A LYS 3.3 16.4 - - - -
228A LYS* 3.6 24.1 - - + +
229A THR* 4.4 0.2 - - - -
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Residues in contact with GLN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 2.5 32.3 + - - +
203A ASN* 4.7 3.0 - - - +
205A TYR* 1.3 78.0 + - - +
207A ILE* 1.3 66.3 + - - +
208A ILE* 3.5 7.2 + - + +
226A TYR* 4.1 3.1 - - - -
227A LYS* 2.6 40.3 + - + +
229A THR* 4.8 12.8 - - + +
314A ILE* 5.6 5.4 - - - +
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASN* 3.9 23.3 - - - +
186A ARG* 5.2 1.8 - - - +
206A GLN* 1.3 75.3 - - - +
208A ILE* 1.3 63.0 + - - +
209A SER 3.8 17.5 - - - +
210A VAL* 4.1 12.3 - - + -
224A ILE* 3.8 24.9 - - + -
225A ILE 3.3 11.7 - - - +
226A TYR* 3.6 26.0 - - + +
317A SER* 4.8 3.3 + - - +
318A LEU* 3.1 17.8 - - + +
567A ILE* 3.7 37.9 - - + +
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Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LYS* 4.0 12.1 - - - +
206A GLN* 3.9 7.4 - - + +
207A ILE* 1.3 78.6 - - - +
209A SER* 1.3 69.3 + - - +
225A ILE* 2.9 26.7 + - + +
227A LYS* 3.5 44.2 - - + -
317A SER 4.7 7.6 - - - +
318A LEU* 3.4 10.9 - - - +
319A LYS* 2.6 37.7 + - + +
286B GLU* 3.8 26.7 - - + +
289B ASP* 4.4 3.4 - - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 3.7 2.8 - - - +
208A ILE* 1.3 93.1 + - - +
210A VAL* 1.3 66.3 + - - +
224A ILE* 3.3 5.7 - - - +
225A ILE* 3.0 36.6 + - - +
318A LEU* 5.3 0.9 - - - -
319A LYS* 3.7 3.1 - - - +
320A TYR* 3.1 35.5 + - - -
286B GLU* 5.6 0.3 - - - +
289B ASP* 5.3 0.9 + - - -
293B PHE* 3.6 24.2 - - - -
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 3.9 12.3 - - - +
207A ILE* 4.1 7.2 - - + -
209A SER* 1.3 80.3 - - - +
211A SER* 1.3 69.8 + - - +
222A ASP* 4.2 2.7 - - - +
223A PHE 3.7 3.4 - - - -
224A ILE* 3.9 19.5 - - + -
318A LEU* 5.2 4.7 - - + -
320A TYR 2.9 9.9 + - - +
322A TYR* 3.0 28.1 + - - +
323A HIS* 3.8 23.1 - - + -
326A TYR* 4.8 12.1 - - + +
567A ILE* 3.7 28.3 - - + -
568A PRO 4.7 1.8 - - - +
293B PHE* 3.9 5.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il